Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/VarscanHit_WithTag.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/VarscanHit_WithTag.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,70 @@ +# Copyright INRA (Institut National de la Recherche Agronomique) +# http://www.inra.fr +# http://urgi.versailles.inra.fr +# +# This software is governed by the CeCILL license under French law and +# abiding by the rules of distribution of free software. You can use, +# modify and/ or redistribute the software under the terms of the CeCILL +# license as circulated by CEA, CNRS and INRIA at the following URL +# "http://www.cecill.info". +# +# As a counterpart to the access to the source code and rights to copy, +# modify and redistribute granted by the license, users are provided only +# with a limited warranty and the software's author, the holder of the +# economic rights, and the successive licensors have only limited +# liability. +# +# In this respect, the user's attention is drawn to the risks associated +# with loading, using, modifying and/or developing or reproducing the +# software by the user in light of its specific status of free software, +# that may mean that it is complicated to manipulate, and that also +# therefore means that it is reserved for developers and experienced +# professionals having in-depth computer knowledge. Users are therefore +# encouraged to load and test the software's suitability as regards their +# requirements in conditions enabling the security of their systems and/or +# data to be ensured and, more generally, to use and operate it in the +# same conditions as regards security. +# +# The fact that you are presently reading this means that you have had +# knowledge of the CeCILL license and that you accept its terms. + + + +from commons.core.parsing.VarscanHit import VarscanHit + +class VarscanHit_WithTag(VarscanHit): + + def __init__(self, tag = "", chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""): + self._tag = tag + VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue) + + def __eq__(self, o): + if self._tag == o._tag: + return VarscanHit.__eq__(self, o) + return False + + def setTag(self, tag): + self._tag = tag + + def getTag(self): + return self._tag + + def getHeader(self): + return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tTag\n" + + def getVarscanLine(self): + return "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getVar(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(), self.getQualRef(), self.getQualVar(), self.getPValue(), self.getTag()) + + def setAttributes(self, lResults, iCurrentLineNumber): + VarscanHit.setAttributes(self, lResults, iCurrentLineNumber) + if lResults[12] != '': + self.setTag(lResults[12]) + + def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"): + varscanString = varscanString.rstrip() + lvarscanStringItem = varscanString.split(fieldSeparator) + if len(lvarscanStringItem)<13: + for i in range(len(lvarscanStringItem), 13): + lvarscanStringItem.append ("") + self.setAttributes(lvarscanStringItem, iCurrentLineNumber) + \ No newline at end of file